@Override public int getEffectiveSizeC() { return getReader().getEffectiveSizeC(); }
@Override public int getEffectiveSizeC() { return getReader().getEffectiveSizeC(); }
sb.append(" ("); boolean first = true; if (r.getEffectiveSizeC() > 1) { sb.append(r.getEffectiveSizeC()); sb.append("C"); first = false;
/** * Gets the Z, C and T coordinates corresponding * to the given rasterized index value (real sizes). */ public static int[] getZCTCoords(IFormatReader reader, int index) { String order = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int num = reader.getImageCount(); return getZCTCoords(order, zSize, cSize, tSize, num, index); }
/** * Gets the rasterized index corresponding * to the given Z, C and T coordinates (real sizes). */ public static int getIndex(IFormatReader reader, int z, int c, int t) { String order = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int num = reader.getImageCount(); return getIndex(order, zSize, cSize, tSize, num, z, c, t); }
/** * Gets the Z, C and T coordinates corresponding * to the given rasterized index value (real sizes). */ public static int[] getZCTCoords(IFormatReader reader, int index) { String order = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int num = reader.getImageCount(); return getZCTCoords(order, zSize, cSize, tSize, num, index); }
/** * Gets the rasterized index corresponding * to the given Z, C and T coordinates (real sizes). */ public static int getIndex(IFormatReader reader, int z, int c, int t) { String order = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int num = reader.getImageCount(); return getIndex(order, zSize, cSize, tSize, num, z, c, t); }
/** * Converts index from the given dimension order to the reader's native one. * This method is useful for shuffling the planar order around * (rather than eassigning ZCT sizes as {@link DimensionSwapper} does). * * @throws FormatException Never actually thrown. */ public static int getReorderedIndex(IFormatReader reader, String newOrder, int newIndex) throws FormatException { String origOrder = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int num = reader.getImageCount(); return getReorderedIndex(origOrder, newOrder, zSize, cSize, tSize, num, newIndex); }
/** * Converts index from the given dimension order to the reader's native one. * This method is useful for shuffling the planar order around * (rather than eassigning ZCT sizes as {@link DimensionSwapper} does). * * @throws FormatException Never actually thrown. */ public static int getReorderedIndex(IFormatReader reader, String newOrder, int newIndex) throws FormatException { String origOrder = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int num = reader.getImageCount(); return getReorderedIndex(origOrder, newOrder, zSize, cSize, tSize, num, newIndex); }
length = reader.getRGBChannelCount(); else if (reader.isIndexed() && reader.getEffectiveSizeC() == 1) { if (reader.getEffectiveSizeC() > 1) { meta.setIndexed(reader.isIndexed()); AxisType type = null; axisLengths.add((long) reader.getEffectiveSizeC());
for (int s=0; s<getSeriesCount(); s++) { setSeries(s); int rgbChannels = getSizeC() / reader.getEffectiveSizeC(); if (rgbChannels == 1) { continue; for (int c=0; c<reader.getEffectiveSizeC(); c++) { int cIndex = c * rgbChannels; if (cIndex >= retrieve.getChannelCount(s)) {
for (int s=0; s<getSeriesCount(); s++) { setSeries(s); int rgbChannels = getSizeC() / reader.getEffectiveSizeC(); if (rgbChannels == 1) { continue; for (int c=0; c<reader.getEffectiveSizeC(); c++) { if (c * rgbChannels >= retrieve.getChannelCount(s)) { break;
@Override public byte[] openThumbBytes(int no) throws FormatException, IOException { FormatTools.assertId(getCurrentFile(), true, 2); int source = getOriginalIndex(no); byte[] thumb = reader.openThumbBytes(source); int c = getSizeC() / reader.getEffectiveSizeC(); int channel = no % c; int bpp = FormatTools.getBytesPerPixel(getPixelType()); return ImageTools.splitChannels(thumb, channel, c, bpp, false, reader.isInterleaved()); }
@Override public byte[] openThumbBytes(int no) throws FormatException, IOException { FormatTools.assertId(getCurrentFile(), true, 2); int source = getOriginalIndex(no); byte[] thumb = reader.openThumbBytes(source); int c = getSizeC() / reader.getEffectiveSizeC(); int channel = no % c; int bpp = FormatTools.getBytesPerPixel(getPixelType()); return ImageTools.splitChannels(thumb, channel, c, bpp, false, reader.isInterleaved()); }
int c = getSizeC() / reader.getEffectiveSizeC(); int source = getOriginalIndex(no); int channel = no % c;
int c = getSizeC() / reader.getEffectiveSizeC(); int source = getOriginalIndex(no); int channel = no % c;
/** * Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates * corresponding to the given rasterized index value (effective * sizes). Note that the Z, C and T coordinates are not the same as * those returned by getZCTCoords(IFormatReader, int) because the * size of the modulo dimensions is taken into account. The * effective size for each of these dimensions is limited to the * total size of the dimension divided by the modulo size. */ public static int[] getZCTModuloCoords(IFormatReader reader, int index) { String order = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int moduloZSize = reader.getModuloZ().length(); int moduloCSize = reader.getModuloC().length(); int moduloTSize = reader.getModuloT().length(); int num = reader.getImageCount(); return getZCTCoords(order, zSize, cSize, tSize, moduloZSize, moduloCSize, moduloTSize, num, index); }
/** * Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates * corresponding to the given rasterized index value (effective * sizes). Note that the Z, C and T coordinates are not the same as * those returned by getZCTCoords(IFormatReader, int) because the * size of the modulo dimensions is taken into account. The * effective size for each of these dimensions is limited to the * total size of the dimension divided by the modulo size. */ public static int[] getZCTModuloCoords(IFormatReader reader, int index) { String order = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int moduloZSize = reader.getModuloZ().length(); int moduloCSize = reader.getModuloC().length(); int moduloTSize = reader.getModuloT().length(); int num = reader.getImageCount(); return getZCTCoords(order, zSize, cSize, tSize, moduloZSize, moduloCSize, moduloTSize, num, index); }
/** * Gets the rasterized index corresponding to the given Z, C, T, * ModuloZ, ModuloC and ModuloT coordinates (effective sizes). Note * that the Z, C and T coordinates take the modulo dimension sizes * into account. The effective size for each of these dimensions is * limited to the total size of the dimension divided by the modulo * size. */ public static int getIndex(IFormatReader reader, int z, int c, int t, int moduloZ, int moduloC, int moduloT) { String order = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int moduloZSize = reader.getModuloZ().length(); int moduloCSize = reader.getModuloC().length(); int moduloTSize = reader.getModuloT().length(); int num = reader.getImageCount(); return getIndex(order, zSize, cSize, tSize, moduloZSize, moduloCSize, moduloTSize, num, z, c, t, moduloZ, moduloC, moduloT); }
/** * Gets the rasterized index corresponding to the given Z, C, T, * ModuloZ, ModuloC and ModuloT coordinates (effective sizes). Note * that the Z, C and T coordinates take the modulo dimension sizes * into account. The effective size for each of these dimensions is * limited to the total size of the dimension divided by the modulo * size. */ public static int getIndex(IFormatReader reader, int z, int c, int t, int moduloZ, int moduloC, int moduloT) { String order = reader.getDimensionOrder(); int zSize = reader.getSizeZ(); int cSize = reader.getEffectiveSizeC(); int tSize = reader.getSizeT(); int moduloZSize = reader.getModuloZ().length(); int moduloCSize = reader.getModuloC().length(); int moduloTSize = reader.getModuloT().length(); int num = reader.getImageCount(); return getIndex(order, zSize, cSize, tSize, moduloZSize, moduloCSize, moduloTSize, num, z, c, t, moduloZ, moduloC, moduloT); }